Package 'PheValuator'

Compute performance metrics based on a 2-by-2 counts table

Description

Compute performance metrics based on a 2-by-2 counts table

Usage

computePerformanceMetricsFromCounts(counts)

Arguments

counts

Counts as created by the testPhenotypeAlgorithm function.

Value

A tibble with the statistics metrics added to the counts table.

Examples

counts <- tibble::tibble(
  truePositives = 120,
  trueNegatives = 800,
  falsePositives = 30,
  falseNegatives = 50,
  cutPoint = "EV"
)
computePerformanceMetricsFromCounts(counts)

---

Create a parameter object for the function createEvaluationCohort

Description

Create a parameter object for the function createEvaluationCohort

Usage

createCreateEvaluationCohortArgs(
  xSpecCohortId,
  daysFromxSpec = 0,
  xSensCohortId = prevalenceCohortId,
  prevalenceCohortId,
  caseCohortId = prevalenceCohortId,
  caseFirstOccurrenceOnly = TRUE,
  xSpecCohortSize = 5000,
  covariateSettings = createDefaultCovariateSettings(excludedCovariateConceptIds = c(),
    addDescendantsToExclude = TRUE),
  modelPopulationCohortId = 0,
  modelPopulationCohortIdStartDay = 0,
  modelPopulationCohortIdEndDay = 0,
  inclusionEvaluationCohortId = 0,
  inclusionEvaluationDaysFromStart = 0,
  inclusionEvaluationDaysFromEnd = 0,
  duringInclusionEvaluationOnly = FALSE,
  exclusionEvaluationCohortId = 0,
  exclusionEvaluationDaysFromStart = 0,
  exclusionEvaluationDaysFromEnd = 0,
  minimumOffsetFromStart = 0,
  minimumOffsetFromEnd = 30,
  modelBaseSampleSize = 25000,
  baseSampleSize = 2e+06,
  lowerAgeLimit = 0,
  upperAgeLimit = 120,
  visitLength = 0,
  visitType = c(9201, 9202, 9203, 581477, 262),
  gender = c(8507, 8532),
  race = 0,
  ethnicity = 0,
  startDate = "19001010",
  endDate = "21000101",
  falsePositiveNegativeSubjects = 10,
  modelId = "main",
  evaluationCohortId = "main",
  randomVisitTable = "",
  excludeModelFromEvaluation = FALSE,
  removeSubjectsWithFutureDates = TRUE,
  saveEvaluationCohortPlpData = FALSE
)

Arguments

xSpecCohortId	The number of the "extremely specific (xSpec)" cohortdefinition id in the cohort table (for noisy positives).
daysFromxSpec	Number of days from xSpec condition until analyzed visit
xSensCohortId	The number of the "extremely sensitive (xSens)" cohortdefinition id in the cohort table (for noisy negatives).
prevalenceCohortId	The number of the cohort definition id to determine the disease prevalence.
caseCohortId	The number of the cohort definition id to determine cases in the evaluation cohort
caseFirstOccurrenceOnly	Set to true if only the first occurrence per subject in the case cohort is to be used
xSpecCohortSize	Maximum xSpec sample size to use in the analysis
covariateSettings	A covariateSettings object as generated using createCovariateSettings().
modelPopulationCohortId	The number of the cohort to be used as a base population for the model. If set to 0, the entire database population will be used.
modelPopulationCohortIdStartDay	The number of days relative to the mainPopulationCohortId cohort start date to begin including visits.
modelPopulationCohortIdEndDay	The number of days relative to the mainPopulationCohortId cohort start date to end including visits.
inclusionEvaluationCohortId	The number of the cohort of the population to be used to designate which visits are are eligible to be in the evaluation cohort
inclusionEvaluationDaysFromStart	The number of days from the cohort start date of the inclusionEvaluationCohortId to start eligible included visits
inclusionEvaluationDaysFromEnd	The number of days from the cohort start date of the inclusionEvaluationCohortId to end eligible included visits
duringInclusionEvaluationOnly	Only include visits that are within the cohort start and end dates
exclusionEvaluationCohortId	The number of the cohort of the population to be used to designate which visits are NOT eligible to be in the evaluation cohort
exclusionEvaluationDaysFromStart	The number of days from the cohort start date of the exclusionEvaluationCohortId to start ineligible included visits
exclusionEvaluationDaysFromEnd	The number of days from the cohort start date of the exclusionEvaluationCohortId to end ineligible included visits
minimumOffsetFromStart	Minimum number of days to offset for the analysis visit from the start of the observation period
minimumOffsetFromEnd	Minimum number of days to offset for the analysis visit from the end of the observation period
modelBaseSampleSize	The number of non-xSpec subjects to include in the model
baseSampleSize	The maximum number of subjects in the evaluation cohort.
lowerAgeLimit	The lower age for subjects in the model.
upperAgeLimit	The upper age for subjects in the model.
visitLength	The minimum length of index visit for acute outcomes.
visitType	The concept_id for the visit type.
gender	The gender(s) to be included.
race	The race(s) to be included.
ethnicity	The ethnicity(s) to be included.
startDate	The starting date for including subjects in the model.
endDate	The ending date for including subjects in the model.
falsePositiveNegativeSubjects	Number of subjects to include for evaluating false positives and negatives
modelId	A string used to generate the file names for this model.
evaluationCohortId	A string used to generate the file names for this evaluation cohort.
randomVisitTable	Table stored in work directory with pre-selected random visits in format of visit_occurrence table
excludeModelFromEvaluation	Should subjects used in the model be excluded from the evaluation cohort?
removeSubjectsWithFutureDates	For buggy data with data in the future: ignore subjects with dates in the future?
saveEvaluationCohortPlpData	Should the large PLP file for the evaluation cohort be saved? To be used for debugging purposes.

Details

Create an object defining the parameter values.

Value

A list of class "args" containing all the provided parameters. This object is used as an argument to the createEvaluationCohort function.

Examples

evalCohortArgs <- createCreateEvaluationCohortArgs(
  xSpecCohortId = 1,
  prevalenceCohortId = 3
)

---

Create the default covariate settings

Description

Create the default covariate settings for acute or chronic diseases

Usage

createDefaultCovariateSettings(
  excludedCovariateConceptIds = c(),
  includedCovariateIds = c(),
  includedCovariateConceptIds = c(),
  addDescendantsToExclude = FALSE,
  startDayWindow1 = 0,
  endDayWindow1 = 9999,
  startDayWindow2 = NULL,
  endDayWindow2 = NULL,
  startDayWindow3 = NULL,
  endDayWindow3 = NULL
)

Arguments

excludedCovariateConceptIds	A list of conceptIds to exclude from featureExtraction. These should include all concept_ids that were used to define the xSpec model (default=NULL)
includedCovariateIds	A list of covariate IDs that should be restricted to.
includedCovariateConceptIds	A list of covariate concept IDs that should be restricted to.
addDescendantsToExclude	Should descendants of excluded concepts also be excluded? (default=FALSE)
startDayWindow1	The day to start time window 1 for feature extraction
endDayWindow1	The day to end time window 1 for feature extraction
startDayWindow2	The day to start time window 2 for feature extraction
endDayWindow2	The day to end time window 2 for feature extraction
startDayWindow3	The day to start time window 3 for feature extraction
endDayWindow3	The day to end time window 3 for feature extraction #'

Details

Function to create the default covariate settings for acute or chronic diseases

Value

A list containing one or more covariate settings objects from the FeatureExtraction package. If only the first time window is specified, returns a list with one element. If additional time windows are specified, returns a list with multiple elements.

Examples

covSettings <- createDefaultCovariateSettings(
  excludedCovariateConceptIds = c(201826, 44786627),
  addDescendantsToExclude = TRUE
)

---

Create the evaluation cohort

Description

Create the evaluation cohort

Usage

createEvaluationCohort(
  connectionDetails,
  oracleTempSchema = NULL,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  phenotype,
  analysisName,
  runDateTime,
  databaseId,
  xSpecCohortId,
  daysFromxSpec = 0,
  xSensCohortId,
  prevalenceCohortId,
  caseCohortId,
  caseFirstOccurrenceOnly,
  xSpecCohortSize = 5000,
  cdmDatabaseSchema,
  cohortDatabaseSchema,
  cohortTable,
  workDatabaseSchema,
  covariateSettings = createDefaultCovariateSettings(excludedCovariateConceptIds = c(),
    addDescendantsToExclude = TRUE),
  modelPopulationCohortId = 0,
  modelPopulationCohortIdStartDay = 0,
  modelPopulationCohortIdEndDay = 0,
  inclusionEvaluationCohortId = 0,
  inclusionEvaluationDaysFromStart = 0,
  inclusionEvaluationDaysFromEnd = 0,
  duringInclusionEvaluationOnly = FALSE,
  exclusionEvaluationCohortId = 0,
  exclusionEvaluationDaysFromStart = 0,
  exclusionEvaluationDaysFromEnd = 0,
  priorModelToUse = NULL,
  minimumOffsetFromStart = 365,
  minimumOffsetFromEnd = 365,
  modelBaseSampleSize = 25000,
  baseSampleSize = 2e+06,
  lowerAgeLimit = 0,
  upperAgeLimit = 120,
  visitLength = 0,
  visitType = c(9201, 9202, 9203, 262, 581477),
  gender = c(8507, 8532),
  race = 0,
  ethnicity = 0,
  startDate = "19001010",
  endDate = "21000101",
  falsePositiveNegativeSubjects = 10,
  cdmVersion = "5",
  outFolder,
  exportFolder,
  modelId = "main",
  evaluationCohortId = "main",
  excludeModelFromEvaluation = FALSE,
  randomVisitTable = "",
  removeSubjectsWithFutureDates = TRUE,
  saveEvaluationCohortPlpData = FALSE
)

Arguments

connectionDetails	connectionDetails created using the function createConnectionDetails in the DatabaseConnector package.
oracleTempSchema	DEPRECATED: use tempEmulationSchema instead.
tempEmulationSchema	Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.
phenotype	Name of the phenotype for analysis
analysisName	Name of the analysis
runDateTime	Starting date and time of the PheValuator run
databaseId	Name of the database in the analysis
xSpecCohortId	The number of the "extremely specific (xSpec)" cohort definition id in the cohort table (for noisy positives).
daysFromxSpec	Number of days allowed from xSpec condition until analyzed visit
xSensCohortId	The number of the "extremely sensitive (xSens)" cohort definition id in the cohort table (for noisy negatives).
prevalenceCohortId	The number of the cohort definition id to determine the disease prevalence.
caseCohortId	The number of the cohort definition id to determine cases in the evaluation cohort
caseFirstOccurrenceOnly	Set to true if only the first occurrence per subject in the case cohort is to be used
xSpecCohortSize	The recommended xSpec sample size to use in model (default = NULL)
cdmDatabaseSchema	The name of the database schema that contains the OMOP CDM instance. Requires read permissions to this database. On SQL Server, this should specifiy both the database and the schema, so for example 'cdm_instance.dbo'.
cohortDatabaseSchema	The name of the database schema that is the location where the cohort data used to define the at risk cohort is available. Requires read permissions to this database.
cohortTable	The tablename that contains the at risk cohort. The expectation is cohortTable has format of COHORT table: cohort_concept_id, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
workDatabaseSchema	The name of the database schema that is the location where a table can be created and afterwards removed. Requires write permissions to this database.
covariateSettings	A covariateSettings object as generated using createCovariateSettings().
modelPopulationCohortId	The number of the cohort to be used as a base population for the model. If set to 0, the entire database population will be used.
modelPopulationCohortIdStartDay	The number of days relative to the mainPopulationCohortId cohort start date to begin including visits.
modelPopulationCohortIdEndDay	The number of days relative to the mainPopulationCohortId cohort start date to end including visits.
inclusionEvaluationCohortId	The number of the cohort of the population to be used to designate which visits are eligible to be in the evaluation cohort
inclusionEvaluationDaysFromStart	The number of days from the cohort start date of the inclusionEvaluationCohortId to start eligible included visits
inclusionEvaluationDaysFromEnd	The number of days from the cohort start date of the inclusionEvaluationCohortId to end eligible included visits
duringInclusionEvaluationOnly	Only include visits that are within the cohort start and end dates
exclusionEvaluationCohortId	The number of the cohort of the population to be used to designate which visits are NOT eligible to be in the evaluation cohort
exclusionEvaluationDaysFromStart	The number of days from the cohort start date of the exclusionEvaluationCohortId to start ineligible included visits
exclusionEvaluationDaysFromEnd	The number of days from the cohort start date of the exclusionEvaluationCohortId to end ineligible included visits
priorModelToUse	folder where a previously developed model to use in analysis will be found
minimumOffsetFromStart	Minimum number of days to offset for the analysis visit from the start of the observation period
minimumOffsetFromEnd	Minimum number of days to offset for the analysis visit from the end of the observation period
modelBaseSampleSize	The number of non-xSpec subjects to include in the model
baseSampleSize	The maximum number of subjects in the evaluation cohort.
lowerAgeLimit	The lower age for subjects in the model.
upperAgeLimit	The upper age for subjects in the model.
visitLength	The minimum length of index visit for acute outcomes.
visitType	The concept_id for the visit type.
gender	The gender(s) to be included.
race	The race(s) to be included.
ethnicity	The ethnicity(s) to be included.
startDate	The starting date for including subjects in the model.
endDate	The ending date for including subjects in the model.
falsePositiveNegativeSubjects	Number of subjects to include for evaluating false positives and negatives
cdmVersion	The CDM version of the database.
outFolder	The folder where the output files will be written.
exportFolder	The folder where the csv output files will be written.
modelId	A string used to generate the file names for this model.
evaluationCohortId	A string used to generate the file names for this evaluation cohort.
excludeModelFromEvaluation	Should subjects used in the model be excluded from the evaluation cohort?
randomVisitTable	Table stored in work directory with pre-selected random visits in format of visit_occurrence table
removeSubjectsWithFutureDates	For buggy data with data in the future: ignore subjects with dates in the future?
saveEvaluationCohortPlpData	Should the large PLP file for the evaluation cohort be saved? To be used for debugging purposes.

Details

Fits a diagnostic prediction model, and uses it to create an evaluation cohort with probabilities for the health outcome of interest.

Value

No return value, called for side effects. Creates database tables and output files containing the predictive model and evaluation cohort data with predicted probabilities for the health outcome.

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(
  dbms = "postgresql",
  server = "myserver",
  user = "user",
  password = "password"
)
createEvaluationCohort(
  connectionDetails = connectionDetails,
  phenotype = "Diabetes",
  analysisName = "Main",
  runDateTime = format(Sys.time(), "%b %d %Y %X"),
  databaseId = "myDB",
  xSpecCohortId = 1,
  xSensCohortId = 2,
  prevalenceCohortId = 3,
  caseCohortId = 3,
  caseFirstOccurrenceOnly = TRUE,
  cdmDatabaseSchema = "cdm.dbo",
  cohortDatabaseSchema = "results.dbo",
  cohortTable = "cohort",
  workDatabaseSchema = "scratch.dbo",
  outFolder = tempdir(),
  exportFolder = file.path(tempdir(), "export")
)

## End(Not run)

---

Create a PheValuator analysis specification

Description

Create a PheValuator analysis specification

Usage

createPheValuatorAnalysis(
  analysisId,
  description,
  createEvaluationCohortArgs,
  testPhenotypeAlgorithmArgs
)

Arguments

analysisId	An integer that will be used later to refer to this specific set of analysis choices.
description	A short description of the analysis.
createEvaluationCohortArgs	An object representing the arguments to be used when calling the createCreateEvaluationCohortArgs function.
testPhenotypeAlgorithmArgs	Should the createTestPhenotypeAlgorithmArgs function be used in this analysis?

Details

Create a set of analysis choices, to be used with the runPheValuatorAnalyses function.

Value

A list object of class "pheValuatorAnalysis" containing the analysis specification. Includes the analysis ID, description, and argument specifications for creating the evaluation cohort and testing the phenotype algorithm.

Examples

evalCohortArgs <- createCreateEvaluationCohortArgs(
  xSpecCohortId = 1,
  xSensCohortId = 2,
  prevalenceCohortId = 3
)
testArgs <- createTestPhenotypeAlgorithmArgs(
  phenotypeCohortId = 10
)
analysis <- createPheValuatorAnalysis(
  analysisId = 1,
  description = "Main analysis",
  createEvaluationCohortArgs = evalCohortArgs,
  testPhenotypeAlgorithmArgs = testArgs
)

---

Create a parameter object for the function testPhenotypeAlgorithm

Description

Create a parameter object for the function testPhenotypeAlgorithm

Usage

createTestPhenotypeAlgorithmArgs(
  cutPoints = c("EV"),
  phenotypeCohortId,
  washoutPeriod = 0,
  splayPrior = 7,
  splayPost = 7
)

Arguments

cutPoints	A list of threshold predictions for the evaluations. Include "EV" for the expected value
phenotypeCohortId	The ID of the cohort to evaluate in the specified cohort table.
washoutPeriod	The mininum required continuous observation time prior to index date for subjects within the cohort to test (Default = 0).
splayPrior	The number of days to allow for test phenotype visit date prior to evaluation date
splayPost	The number of days to allow for test phenotype visit date after evaluation date

Details

Create an object defining the parameter values.

Value

A list object of class "args" containing all the provided parameters. This object is used as an argument to the testPhenotypeAlgorithm function.

Examples

testArgs <- createTestPhenotypeAlgorithmArgs(
  phenotypeCohortId = 10,
  cutPoints = c("EV", "0.5")
)

---

Load a list of phevaluatorAnalysis from file

Description

Load a list of objects of type pheValuatorAnalysis from file. The file is in JSON format.

Usage

loadPheValuatorAnalysisList(file)

Arguments

file	The name of the file

Value

A list of objects of type pheValuatorAnalysis.

Examples

## Not run: 
analysisList <- loadPheValuatorAnalysisList(file = "analysisList.json")

## End(Not run)

---

Run a list of analyses

Description

Run a list of analyses

Usage

runPheValuatorAnalyses(
  phenotype,
  cohortDefinitionSet = data.frame(),
  analysisName = "Main",
  runDateTime = format(Sys.time(), "%b %d %Y %X"),
  connectionDetails,
  oracleTempSchema = NULL,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  cdmDatabaseSchema,
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTable = "cohort",
  workDatabaseSchema = cdmDatabaseSchema,
  databaseId = cdmDatabaseSchema,
  cdmVersion = 5,
  outputFolder,
  priorModelToUse = NULL,
  pheValuatorAnalysisList
)

Arguments

phenotype	Name of the phenotype for analysis
cohortDefinitionSet	Data.frame of cohorts must include columns cohortId, cohortName, json, sql - should include all cohort definitions needed to replicate PheValuator analysis
analysisName	Name of the analysis
runDateTime	Starting date and time of the PheValuator run
connectionDetails	An R object of type connectionDetails created using the function createConnectionDetails in the DatabaseConnector package.
oracleTempSchema	DEPRECATED: use tempEmulationSchema instead.
tempEmulationSchema	Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.
cdmDatabaseSchema	The name of the database schema that contains the OMOP CDM instance. Requires read permissions to this database. On SQL Server, this should specifiy both the database and the schema, so for example 'cdm_instance.dbo'.
cohortDatabaseSchema	The name of the database schema that is the location where the cohort data used to define the at risk cohort is available. Requires read permissions to this database.
cohortTable	The tablename that contains the at risk cohort. The expectation is cohortTable has format of COHORT table: cohort_concept_id, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
workDatabaseSchema	The name of the database schema that is the location where a table can be created and afterwards removed. Requires write permissions to this database.
databaseId	Name of the database in the analysis
cdmVersion	Define the OMOP CDM version used: currently supports "5".
outputFolder	Name of the folder where all the outputs will be written to.
priorModelToUse	folder where a previously developed model to use in analysis will be found
pheValuatorAnalysisList	A list of objects of type pheValuatorAnalysis as created using the createPheValuatorAnalysis function.

Details

Run a list of analyses.

Value

A data frame specifying where the constructed evaluation cohort and phenotype evaluation results can be found in the local file system.

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(
  dbms = "postgresql",
  server = "myserver",
  user = "user",
  password = "password"
)
analysisList <- list(
  createPheValuatorAnalysis(
    analysisId = 1,
    description = "Main analysis",
    createEvaluationCohortArgs = createCreateEvaluationCohortArgs(
      xSpecCohortId = 1,
      prevalenceCohortId = 3
    ),
    testPhenotypeAlgorithmArgs = createTestPhenotypeAlgorithmArgs(
      phenotypeCohortId = 10
    )
  )
)
runPheValuatorAnalyses(
  phenotype = "Diabetes",
  connectionDetails = connectionDetails,
  cdmDatabaseSchema = "cdm.dbo",
  outputFolder = tempdir(),
  pheValuatorAnalysisList = analysisList
)

## End(Not run)

---

Save a list of phevaluatorAnalysis to file

Description

Write a list of objects of type pheValuatorAnalysis to file. The file is in JSON format.

Usage

savePheValuatorAnalysisList(pheValuatorAnalysisList, file)

Arguments

pheValuatorAnalysisList	The pheValuatorAnalysis list to be written to file
file	The name of the file where the results will be written

Value

No return value, called for side effects. Writes a JSON file containing the analysis list to the specified file path.

Examples

## Not run: 
# Requires pre-existing analysis list object; example usage:
# savePheValuatorAnalysisList(pheValuatorAnalysisList = myAnalysisList,
#                             file = file.path(tempdir(), "analysisList.json"))

## End(Not run)

---

Summarize results of PheValuator analyses

Description

Summarize results of PheValuator analyses

Usage

summarizePheValuatorAnalyses(referenceTable, outputFolder)

Arguments

referenceTable	A reference table as created using runPheValuatorAnalyses.
outputFolder	The output folder used when calling runPheValuatorAnalyses.

Value

A data frame of results.

Examples

## Not run: 
refTable <- runPheValuatorAnalyses(
  phenotype = "Diabetes",
  connectionDetails = connectionDetails,
  cdmDatabaseSchema = "cdm.dbo",
  outputFolder = tempdir(),
  pheValuatorAnalysisList = analysisList
)
results <- summarizePheValuatorAnalyses(refTable, outputFolder = tempdir())

## End(Not run)

---

Test phenotype algorithms

Description

Test phenotype algorithms

Usage

testPhenotypeAlgorithm(
  phenotype,
  analysisName,
  runDateTime,
  connectionDetails,
  cutPoints = c("EV"),
  outFolder,
  exportFolder,
  evaluationCohortId = "main",
  phenotypeCohortId,
  cdmDatabaseSchema,
  databaseId,
  cohortDatabaseSchema,
  cohortTable,
  washoutPeriod = 0,
  splayPrior = 7,
  splayPost = 7
)

Arguments

phenotype	Name of the phenotype for analysis
analysisName	Name of the analysis
runDateTime	Starting date and time of the PheValuator run
connectionDetails	ConnectionDetails created using the function createConnectionDetails in the DatabaseConnector package.
cutPoints	A list of threshold predictions for the evaluations. Include "EV" for the expected value
outFolder	The folder where the cohort evaluation output files are written
exportFolder	The folder where the csv output files will be written.
evaluationCohortId	A string used to generate the file names for the evaluation cohort.
phenotypeCohortId	The ID of the cohort to evaluate in the specified cohort table.
cdmDatabaseSchema	The name of the database schema that contains the OMOP CDM instance. Requires read permissions to this database. On SQL Server, this should specifiy both the database and the schema, so for example 'cdm_instance.dbo'.
databaseId	Name of the database in the analysis
cohortDatabaseSchema	The name of the database schema that is the location where the cohort data used to define the at risk cohort is available. Requires read permissions to this database.
cohortTable	The tablename that contains the at risk cohort. The expectation is cohortTable has format of COHORT table: cohort_concept_id, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
washoutPeriod	The mininum required continuous observation time prior to index date for subjects within the cohort to test (Default = 0).
splayPrior	The number of days to allow for test phenotype visit date prior to evaluation date
splayPost	The number of days to allow for test phenotype visit date after evaluation date

Details

This function will perform the phenotype algorithm evaluation using the evaluation cohort returned from createEvalCohort and the phenotype algorithm cohort specified

Value

A dataframe with the results from the phenotype algorithm evaluation.

If 0.5 is included as a cutpoint, the data frame will have an attribute called 'misses', a dataframe with a sample of subject ids for TPs, FPs, TNs, and FNs for the 50 percent and over prediction threshold.

Examples

## Not run: 
connectionDetails <- DatabaseConnector::createConnectionDetails(
  dbms = "postgresql",
  server = "myserver",
  user = "user",
  password = "password"
)
results <- testPhenotypeAlgorithm(
  phenotype = "Diabetes",
  analysisName = "Main",
  runDateTime = format(Sys.time(), "%b %d %Y %X"),
  connectionDetails = connectionDetails,
  cutPoints = c("EV", "0.5"),
  outFolder = tempdir(),
  exportFolder = file.path(tempdir(), "export"),
  phenotypeCohortId = 10,
  cdmDatabaseSchema = "cdm.dbo",
  databaseId = "myDB",
  cohortDatabaseSchema = "results.dbo",
  cohortTable = "cohort"
)

## End(Not run)

---